How to use reset

Short the reset pin once to enter/restart the actual 16u2 program. Your 16u2 firmware/sketch starts running. By default the program starts when you plug in the USB-Cable. If no program is presented the bootloader will run.

Short the reset pin twice to enter bootloader mode manually. In bootloader mode you can upload code to the 16u2 or the 328/2560. You have full CDC bootloader functions (for the 16u2) and USB-Serial with auto reset (for the main MCU) like on a not modified Arduino. Baud rate 57600 is used for the CDC Bootloader and not available for USB-Serial.

Once you've uploaded your custom program it is possible that you don't have the CDC Serial any more. That might happen if you want to deactivate the USB functions or upload a custom firmware. To flash one of the two MCUs (16u2 or 328/2560) you need to enter bootloader mode again by shorting the reset pin twice.

With HoodLoader2.0.4 it is now possible that you can upload a program for the I/O MCU (328/2560) without manually resetting the 16u2 twice. Select the current COM port and select the HID-Bridge Arduino Uno as board. Hit upload and it should switch to bootloader mode. It will stay in bootloader mode then. If you want to run the 16u2 program again reset the 16u2 once again manually. The COM port number should have changed now. Reset before uploading again or select the new COM port.

In bootloader mode the device enumerates as different USB device than the uploaded program. The HoodLoader2 itself just needs the standard Arduino drivers.